It started with a common enough skirmish in the hotly disputed waters of the South China Sea. Ten days ago, a Philippine coast guard ship went too far in chasing off a Taiwanese fishing vessel in disputed waters. Such actions involve water cannons and the damage is nothing worse than a few broken portholes. This time the coast guard ship loosed off 54 rounds into the side of the Taiwanese boat and killed a fisherman. The Philippines' National Bureau of Investigation launched an inquiry. A spokesmen for President Benigno S Aquino III said that a representative would convey "deep regret and apology" to the family of the dead fisherman. But all of this fell short of an official apology.

Taiwan was having none of it. It gave Manila 72 hours to apologise, failing which it would withdraw its representative and end the visa regime for Filipino workers. All of which it has now done, throwing in a two-day military drill in the channel which divides the two countries, for good measure. On Friday, the Philippine envoy to Taiwan advised Filipino workers there to avoid the streets, as emotions are running high. Then came the second surprise: China applauded. The dispute has been running high on the evening news. Commentators have denounced the Philippines and applauded Taiwan's resolute response.

To receive Beijing's approbation is something of a novelty for Taiwan. Cross-strait relations may be at their warmest for 60 years, (there are now more scheduled flights from Taipei to cities on the mainland than there are from Hong Kong), but even so. Any time Taiwan acts independently in the international arena, Beijing reverts to the orthodoxy of its One China policy. When Taiwan's president, Ma Ying-jeou, reached a pragmatic fishing deal with Japan, which might defuse the tension around the disputed islands which Japan calls the Senkakus and Taiwan knows as the Diaoyutai, China expressed its wrath – but all of it was pointed at Japan, rather than Taipei.

The fishing deal could be used as a template for other disputes. It side-steps the sovereignty debate by establishing a large area around the islands – 74,300 sq km, or twice the size of Taiwan itself – as a jointly managed fishing ground. Japan maintains its territorial waters around the islands, which Taiwanese fishermen cannot enter. But they get in return an area far beyond the 200 miles they once claimed as their exclusive economic zone. These talks have been brewing a long time. There have been 16 rounds of negotiation since 1996. The 17th may have finally been clinched by China's recent naval assertiveness, about which both Japan and Taiwan are wary. By hook or by crook, Taiwan is winning for itself greater regional influence under a leader criticised at home as being too pro-Chinese.